Introduction to Drug Design

Drug Design is the important part of the drug discovery. It is a systematic

approach to finding, selection, optimization of drug molecules on the basic of
molecular interactions (Strero-structural basis) between drug and target proteins
and or its physico-chemical properties involved.

The drug discovery and development are very time and resources consuming
process. Due to the high research & development (R&D) costs and extensive
clinical testing, drug discovery and development has become an expensive
process (Avg cost millions of USD and 10-15 years)

Drug design or rational drug design is the innovative process of finding new drug molecules
based on the knowledge of the biological target.

The drug is mostly an organic molecule which activates or inhibits the function of target
proteins that in turn results in a therapeutic effect.
Frequently the drug design is based on a computer modeling technique known as computer-
aided drug design (CADD).

In CADD attempts are made to find a ligand that will interact favorably with a receptor or
target protein that represents the target site.
Binding of ligand to the receptor may include hydrophobic, electrostatic, and hydrogen-
bonding

The approach used in CADD is dependent upon the amount of information that is available
about the ligand and receptor. Ideally, one would have 3-dimensional structural information
for the receptor and the ligand-receptor complex from X-ray diffraction or NMR.

Based on the information that is available, one can apply either ligand-based or structure
based drug design methods.

Regulatory agencies as well as pharmaceutical industry are actively involved in development

of computational tools that will improve effectiveness and efficiency of drug discovery and
development process, decrease use of animals, and increase predictability. There are two
major types or approaches to drug design.

• Ligand based drug design (Indirect drug design)

• Structure based drug design (Direct drug design)

Ligand based drug design (Indirect drug design): Ligand based drug design is based on
the knowledge of other molecules that bind to the biological target of interest so as to derive a
pharmacophore which will bind to the target.

(A) Q SAR
(B) Analog drug design
(C) Combinatorial chemistry
(D) Natural Products as a lead, etc

Structure based drug design (Direct drug design): Structure based drug design is based on
the knowledge of the three dimensional structure of the biological target. Using the structure
of the biological target, candidate drugs that are predicted to bind with high affinity and
selectivity to the target may be designed.

Various Approaches and Concepts

Drug design seeks to explore:

• ✓ Effects of biological compounds on the basis of molecular interaction

• ✓ Explore the various process involve in drug discovery
• ✓ Explore drug-protein interaction to elicit biological response
• ✓ Probable relationship between biological activity and chemical structure.
 Concept of LEAD

Lead is the prototype bioactive molecule subjected to drug design and drug discovery
and needs to exploration and exploitation.

• Exploration of Lead: The search for new lead.

• Exploitation of Lead: Requires assessment, improvement and extension of lead.

Concept of Analogue

✓ Chemical Derivatives or structural analogue having similar structure with little

medication

Concepts of Prodrug

Prodrug is the appropriative derivatives which converts active metabolite invo

Various Approaches used in Drug Design

The various approaches used in drug design (Ligand based or Structural based) include the
following.
1) Drug discovery via Random screening of synthetic compounds or chemicals and natural
products by bioassay procedures.

2) Drug discovery via metabolic studies

3) Drug discovery via Novel compounds preparation based on the known structures of
biologically active, natural substances of plant and animal origin, i.e., lead skeleton.
4) Drug discovery via Preparation of structural analogs of lead with increasing biological
activity and Application of bio isosteric principle.

Ligand based drug design

Ligand based drug design or indirect drug design is an approach used in the absence of the
receptor 3D information and it based on knowledge of molecules that bind to the biological
target of interest.

A model of the biological target may be built based on the knowledge of what binds to it ????
: Hydrophobic and hydrophillic groups

3D quantitative structure activity relationships (3D QSAR) and pharmacophore modeling

are the most important and widely used tools in ligand based drug design.
They can provide predictive models suitable for lead identification and optimization

Basic Approaches: (A) Q SAR

(B) Analog drug design

(C) Combinatorial chemistry
(D) Natural Products as a lead, etc

A) QSAR(Quantitative Structure Activity Relationships)

QSAR is mathematical or statistical approaches to define the relationship between biological

activity (experimental data) of a molecular system and its geometrical, physical, electronic,
and chemical properties

Activity = function (property 1 , property 2.....)

Activity = function (xi)

xi- descriptor
Property- geometry, steric, or steric etc

B) Analogue Drug Design

Analog design is most fruitful in the study of pharmacologically active molecules that are
structurally specific: their biological activity depends on the nature and the details of their
chemical structure.

QSAR involves the derivation of mathematical formula which relates the biological activities
of a group of compounds to their measurable physicochemical parameters. These parameters
have major influence on the drug’s activity. QSAR derived equation take the general form:

Biological activity= function(parameters)

Activity is expressed as log(1/c). C is the minimum concentration required to cause a defined

biological response.

PARAMETERS

The parameter is the measure of the potential contribution of its group to a particular property
of the parent drug.

Various parameters used in QSAR studies are

1. Lipophilic parameters: partition coefficient, π-substitution constant

2. Polarizability parameters: molar refractivity, parachor

3. Electronic parameters: Hammet constant, dipole moment.

4. Steric parameters: Taft’s constant.

5. Miscellaneous parameters: molecular weight, geometric parameters.

LIPOPHILIC PARAMETERS

Lipophilicity is partitioning of the compound between an aqueous and non-aqueous phase.

Partition coefficient:

P = [drug] in octanol / [drug] in water

Typically over a small range of log P, e.g. 1-4, a straight line is obtained

e.g. log 1/C = 0.75 log P + 2.30

If graph is extended to very high log P values, then get a parabolic curve

log 1/C = - k1 (log P) 2 + k 2log P + k3

When P small, dominated by log P term

When P large, log P squared dominates & so activity decreases

π-substituent constant or hydrophobic substituent constants:

The π-substituent constant defined by hansch and co-workers by the following equation.

px = log Px - log PH

A positive πvalue indicates that the πsubstituent has a higher lipophilicity than hydrogen and
the drug favours the organic phase.

A negative πvalue indicates that the π substituent has a lower lipophilicity than hydrogen and
the drug favours the aqueous phase.

ELECTRONIC PARAMETERS

The Hammett constant( σ);

s x = log (Kx/Kbenzoic )

Electron Withdrawing Groups

Equilibrium shifts Right & Kx > Kbenzoic

Since s x = log K x – log Kbenzoic, then s will be positive .

Hammett constant takes into account both resonance and inductive effects; thus, the value
depends on whether the substituent is para or meta substituted -ortho not measured due to
steric effects.

STERIC SUBSTITUTION CONSTANT

It is a measure of the bulkiness of the group it represents and it effects on the closeness of
contact between the drug and receptor site.

much harder to quantitate

Examples are:

Taft’s steric factor (Es) (~1956), an experimental value based on rate constants

Molar refractivity (MR)--measure of the volume occupied by an atom or group--equation

includes the MW, density, and the index of refraction—

Ver loop steric parameter--computer program uses bond angles, van der Waals radii, bond
lengths

HANSCH ANALYSIS

Proposed that drug action could be divided into 2 stages:

1) Transport & 2) Binding

Each of these stages depend upon the physical and chemical properties of the drug.

Log 1/C = k1P = k 2 P2 + k3s + k 4Es + k5

Look at size and sign for each component of the equation.

Values of r <<0.9 indicate equation not reliable

Accuracy depends on using enough analogs, accuracy of data, & choice of parameters

Applications: used to predict the activity of an as yet un synthesized analouge.

 COMPUTER AIDED DRUG DESIGN(CADD)

Computers are an essential tool in the modern medicinal chemistry and are important in both
drug discovery and development.

MOLECULAR MODELING:

Molecular modeling is a general term that covers a wide range of molecular mechanics and
computational chemistry techniques used to build, display, manipulate, simulate and analyze
molecular structure and to calculate properties of those structures.

Molecular modeling techniques can be divided into molecular graphics and computation
chemistry.

A pharmacophore is a molecular frame that describes the vital features responsible for the
biological activity of a molecule.

Pharmacophore models are generated to increase the understanding about the ligand–protein
interactions.

They can be empolyed in identifying new molecules that satisfy the pharmacophore
requirements and thus expected to be active .

Pharmacophore models can be built by using the structural information about the active
ligands that bind to the target if the target structure is not available. This is known as ligand-
based pharmacophore modeling approach.

In conditions where the structure of the target is available, pharmacophore models can be
built by using the structural properties of the target. This is known as structure-based
pharmacophore modeling approach .

There are several pharmacophore modeling tools in use. HipHop, HypoGen, Pharmer,
PHASE, GASP, PharmaGist, PharmMapper, MOE, LigandScout, and GALAHAD are
examples of softwares used for pharmacophore model generation.

With the use of such softwares, pharmacophore modeling has been employed at the various
stages of the drug discovery process.

Virtual screening, drug target fishing, ligand profiling, docking and ADMET (absorption,
distribution, metabolism, excretion, toxicity) prediction are among its popular application
areas.

The pharmacophore concept was introduced by Paul Ehrlich in the early 1900s. Then, the
term pharmacophore was coined and defined as molecular features that bears (phoros) the
necessary properties for the biological activity of a drug (pharmacon).

In those year’s pharmacophore was understood as chemical or functional groups on a

molecule that are responsible for the biological activity.
IUPAC (International Union of Pure and Applied Chemistry) defined pharmacophore as
the sum of steric and electronic properties that are required for the interaction of a molecule
with a target and thus provide the biological activity .

Pharmacophore is a pattern of features responsible for the biological activity of a

compound. This shows that the concept of pharmacophore is more of about features than
chemical groups. Each atom or group of a compound that shows features associated with
molecular recognition can be converted into a pharmacophore pattern.

Molecular pharmacophore patterns can be hydrogen bond donors (HBD), hydrogen bond
acceptors (HBA), positive features, negative features, aromatic rings, hydrophobic features
and their combinations .

A pharmacophore model includes several patterns arranged in a particular 3D (three

dimensional) pattern. Each pattern is depicted by a typical sphere containing radius that
determines the deviation tolerance from the exact position. There are also various other
displaying ways. These patterns can be displayed as a single pattern or their combinations.

There are two principal approaches of pharmacophore modeling that are used in the drug
discovery process: Ligand-based pharmacophore modeling and structure-based
pharmacophore modeling.

In the ligand-based pharmacophore modeling approach, novel ligands are designed by

using a set of active ligands available. This approach is employed if the target structure is not
available. In a similar manner, the structure-based pharmacophore approach is employed
when the structure of the target protein is available.

In the ligand-based pharmacophore modeling, first active ligands are identified by using
the literature available or database search. The data set is split into a training set and test set.
Then, feature analysis of the training set ligands is done. The common features are detected
through the alignment of the active ligands. The next step is pharmacophore model
generation and ranking of the generated models. Finally, pharmacophore model validation is
performed and the best pharmacophore model is selected depending on the results obtained.

In the structure-based pharmacophore modeling, selection and preparation of target

protein structure is the first step. The second step is binding site prediction. Then,
complemental chemical features of the binding site amino acids and their layouts are
identified by analyzing it carefully. After this, the pharmacophore features, which should be
optimized by the adjusted tools in the programs employed, are generated. Finally, crucial
pharmacophore features responsible for the activity are selected. LigandScout , MOE, Pocket
v2 and Snooker are among the commonly used softwares for structure-based pharmacophore
modeling. Similarly, there are various softwares and servers used in pharmacophore
modeling.
The commonly employed programs and servers are summarized in the alphabetical order
(Table ).

Program/Server Brief Description

CATALYST-HipHop CATALYST is now part of the BIOVIA Discovery Studio. It consists of

algorithms used in pharmacophore generation: HipHop and HypoGen. HipHop
gives the alignment of active ligands against a specific target and finds the
three dimensional arrangements of common features by overlapping various
structures.

CATALYST- It generates hypotheses that are able to estimate the activity of molecules
HypoGen quantitatively by using biological analysis data. Thus, it allows the correlation
of the structural and activity data for pharmacophore modeling.

GALAHAD The program uses modified genetic algorithm and fixes certain shortcomings
of the GASP program and thus increases its performance. It increases the
computational speed by using prebuilt structures as a starting point.

GASP GASP is available in the SYBYL package. It uses genetic algorithm for the
detection of pharmacophores. Unlike the other pharmacophore
determinations, conformational search is carried out instantly in the GASP
process and is an integral part of the program. A single low energy structure
and random spinings are applied to examine conformational changes before
superimposing on each input compound.

LigandScout Though it is possible to perform both structure-based and ligand- based

phamacophore modeling with LigandScout, it is among the first programs
specialized in structure-based pharmacophore modeling. Especially, if the
structure of the target protein is present in its ligand bound state,
LigandScout is widely used.

MOE (27) MOE is able to perform ligand-based and structure-based pharmacophore

modeling. Model building is performed by the pairwise alignment of the active
ligands. It is recommended to decrease the magnitude of the training set by
grouping similar molecules.

PharmaGist It is a freely accessible server used in ligand-based pharmacophore

generation. This web server detects pharmacophores via multiple flexible
alignments of the input molecules.

Pharmer It is a pharmacophore method that makes searching based on the width and
complexity of the query instead of the molecular library screened. It is a very
fast method and its source code is available under an open-source license.
PharmMapper It is a freely accessible web server used for the identification of potential
targets for the input ligands. It calculates pharmacophores by using semi-
rigid pharmacophore mapping.

PHASE It is provided by Schrödinger package. It is a convenient approach used in

drug discovery with or without its receptor structure. It creates a hypothesis
from one or more ligands, protein-ligand complexes and apo proteins. It has
a special algorithm designed for use in optimization of lead compounds and
virtual screening.

Combinatorial Chemistry: The synthesis of chemical compounds as ensembles (libraries)

and the screening of those libraries for compounds with desirable properties.

Potentially speedy route to new drugs, catalysts, and other compounds and materials `
Technique invented in the late 1980s and early 1990s to enable tasks to be applied to many
molecules simultaneously

` Establishment of Libraries

Unbiased libraries (Random libraries)

• Typically a common chemical core (starting point scaffold)

• Large number of building blocks (highly diverse)
• Many targets
• Generating ”lead” structures
• Solid phase synthesis (one bead screening if possible)

Directed libraries

• Again a common chemical core

• Limited number of building blocks (structural similar)
• Directed towards a specific target
• Used to optimize ”lead” structures
• << 5.000 compounds
• Solid phase synthesis, synthesis in solution

SOLID PHASE SYNTHESIS

The reaction is carried out on a solid support such as resin beads. The bead is treated with
different starting materials, which bound together.

Then it is mixed with another reagent to get product.

• Solid support: it is depend upon the type of reaction. Ex: polystyrene

• Linker: that sites between our compound and solid support Ex: wang resin, rink resin

• Protecting groups: these are important for blocking and regenerating certain functional
group in a reaction sequence. Ex: FMOC (9-Fluorenylmethyloxycarbonyl.), TBOC (tert-
butyloxycarbonyl) .

Combinatorial synthesis on solid support is usually carried out using either parallel synthesis
and mix procedures

Parallel synthesis: `

In this method the compounds are prepared in separate vessel but at the same time parallely
mixing and splitting process will take place.

Mix and split technique: `

May be used to make both large and small combinatorial libraries using relatively few
reaction steps. `

The history of the bead is traced by using suitable encoding method or deconvulsion.

SOLUTION PHASE SYNTHESIS

Reaction proceeds in Solution. Can be used to produce libraries that consist of single
compounds or mixtures. `

Single compound libraries are prepared using parallel synthesis. Easy characterization of
intermediates as well as end product. `

No limitations in attachment point . ` Faster validation times relative to solid phase synthesis.

Standard analytical protocols can be used to characterize products between each reaction step

Difficult to drive the reaction towards the product, extensive purification is needed

PARALLEL SYNTHESIS

Each compound is prepared in a specific vessel (on pins or Tea-bags) ƒ

Array of reaction vessels (96 well plates -> each well other compound) ƒ

Automated control of reactions -> easy to keep track of each compound

High yields

Useful for epitope mapping (Epitope mapping is the process of identifying the binding site of
an antibody on its target antigen).

Just applicable when small number of positions are being varied -> small libraries
PREPARATION OF LIBRARIES

Pool/Split Synthesis

Good to generate large libraries

Labeling required to keep track of each compound

Beads (resin) are split into different vessels

Then reacted, shuffled, and split again.

1000 compund library prepared from 10 building blocks in each step Æ 30 reaction steps.
(1110 steps for parallel synthesis)

HIGH THROUGHPUT SCREENING

Combinatorial synthesis produces a large quantity of structure in a very short time period,
biological testing should be carried out quickly and automatically. The technique used by this
system is known as HTS.

Compounds are automatically tested and analyzed on a plate containing 96 small wells with
the capacity of 0.1ml .

In HTS 1536 well with capacity of 1-10μl only used.

APPLICATIONS

Drug Discovery - Lead Optimization.

Lead identification libraries < 10 000.

Lead optimization libraries 1000-2000.

Lead optimization via focussed libraries based on a privileged structure.

Both solution and solid-phase synthesis.